Microbiome data analysis
…BRIEF INTRO IN PROGRESS…
IMAP-PART 01
Software requirement for microbiome data analysis
IMAP-PART 02
Exploring and profiling SRA sample metadata
IMAP-PART 03
Downloading SRA FastQ reads using fasterq-dump
IMAP-PART 04
Quality Control of Sequencing Reads
IMAP-PART 05
Microbial profiling with MOTHUR pipeline
IMAP-PART 06
Microbial profiling with QIIME2 pipeline
IMAP-PART 07
Microbial & functional profiling with BIOBAKERY pipelines
Multi-Omics data analysis
…BRIEF INTRO IN PROGRESS…
Citation
Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.
References
[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C.,
Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated
bioinformatics and visualization pipeline for microbiome data analysis.
BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
Appendix
Project main tree
.
├── LICENSE
├── README.md
├── config
│ └── config.yml
├── dags
│ ├── rulegraph.png
│ └── rulegraph.svg
├── images
│ ├── bioinformatics.png
│ ├── bkgd.png
│ ├── imap.png
│ ├── imap_part01.svg
│ ├── imap_part02.svg
│ ├── imap_part03.svg
│ ├── imap_part04.svg
│ ├── imap_part05.svg
│ ├── imap_part06.svg
│ ├── imap_part07.svg
│ ├── rulegraph.png
│ └── smkreport
├── index.Rmd
├── library
│ ├── apa.csl
│ ├── export.bib
│ ├── imap.bib
│ └── references.bib
├── report.html
├── results
│ └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
├── Snakefile
├── envs
│ ├── mothur.yml
│ └── qiime220232.yml
├── report
│ ├── biobakery.rst
│ ├── imap.rst
│ ├── mothur.rst
│ ├── qiime2.rst
│ ├── readqc.rst
│ ├── rsmkrpt.rst
│ ├── software.rst
│ ├── sracache.rst
│ ├── srametadata.rst
│ ├── srareads.rst
│ └── workflow.rst
├── rules
│ ├── render_index.smk
│ ├── report.smk
│ └── rules_dag.smk
└── scripts
├── README.md
├── files4smk_report.sh
├── render.R
├── rules_dag.sh
├── smk_html_report.sh
└── tree.sh
12 directories, 48 files
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